Artemis Screenshot of Prodigal Results Compared with Curated Annotations and other Computational Genefinders for Anaeromyxobacter dehalogenans 2CP-C (Click to enlarge)
- Speed: Prodigal is an extremely fast gene recognition tool (written in very vanilla C). It can analyze an entire microbial genome in 30 seconds or less.
- Accuracy: Prodigal is a highly accurate gene finder. It correctly locates the 3' end of every gene in the experimentally verified Ecogene data set (except those containing introns). It possesses a very sophisticated ribosomal binding site scoring system that enables it to locate the translation initiation site with great accuracy (96% of the 5' ends in the Ecogene data set are located correctly).
- Specificity: Prodigal's false positive rate compares favorably with other gene identification programs, and usually falls under 5%.
- GC-Content Indifferent: Prodigal performs well even in high GC genomes, with over a 90% perfect match (5'+3') to the Pseudomonas aeruginosa curated annotations.
- Metagenomic Version: Prodigal can run in metagenomic mode and analyze sequences even when the organism is unknown.
- Ease of Use: Prodigal can be run in one step on a single genomic sequence or on a draft genome containing many sequences. It does not need to be supplied with any knowledge of the organism, as it learns all the properties it needs to on its own.
- Open Source: Prodigal source code is freely available under the General Public License.
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Referencing Prodigal: Hyatt D, Chen GL, Locascio PF, Land ML, Larimer FW, Hauser LJ. Prodigal: prokaryotic gene recognition and translation initiation site identification. BMC Bioinformatics. 2010 Mar 8;11(1):119. (Highly Accessed) Abstract Full Text
Referencing MetaProdigal: Hyatt D, Locascio PF, Hauser LJ, Uberbacher EC. Gene and translation initiation site prediction in metagenomic sequences. Bioinformatics. 2012 Sep 1;28(17):2223-2230. Abstract Full Text